[gmx-users] Re: Problem with minimizing the energy of the solvated system

[Tsjerk Wassenaar]

Hi,

Indeed, it's the 'box-gets-lost-bug'. It happens with the tutorial
because it was written for an earlier gromacs version. There's an
updated one for 4.5.5 at http://md.chem.rug.nl/~mdcourse/molmod2012/

Although I'll check again if that bug may still cause problems... If
you stick to .gro format for structures, you're always fine. Only if
you want to use pymol or so, you need to convert it to .pdb.

Cheers,

Tsjerk

On Fri, Jul 6, 2012 at 6:38 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi,
>
> Indeede, it's the 'box-gets-lost-bug'. It happens with the tutorial because
> it was written for an earlier gromacs version. There's an updated one for
> 4.5.5 at http://md.chem.rug.nl/~mdcourse/molmod2012/
> Although I'll check again if that bug may still cause problems... If you
> stick to .gro format for structures, you're always fine. Only if you want to
> use pymol or so, you need to convert it to .pdb.
>
> Cheers,
>
> Tsjerk
>
> On Jul 5, 2012 11:59 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
>
> On 7/5/12 5:51 PM, jonas87 wrote: > > Protein-water.pdb has the following
> line: > CRYST1   75.324 ...
>
> Sounds about right.
>
>> I'm using the latest version of gromacs, that means this bug was >
>> reintroduced?
>
> Likely it was not fully fixed; I recall a change to editconf, but maybe
> genion needs a look as well.
>
>> So it is ok to always output to .gro instead of .pdb? >
>
> Always.
>
> -Justin -- ======================================== Justin A. Lemkul, Ph.D.
> Research Scientist ...
>
> -- gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-us...



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands